rs609959

Variant names:

• chr1-18719325-G-A
• rs609959
• NM_001135254.2:c.1155+16029G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-18719325-G-A
• chr1-18719325-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135254.2(PAX7):​c.1155+16029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,270 control chromosomes in the GnomAD database, including 61,223 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.90 (61223 hom., cov: 33)
• Consequence: PAX7 NM_001135254.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 2 publications found

Genes affected

PAX7 (HGNC:8621): (paired box 7) This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. The specific function of the paired box 7 gene is unknown but speculated to involve tumor suppression since fusion of this gene with a forkhead domain family member has been associated with alveolar rhabdomyosarcoma. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

PAX7 Gene-Disease associations (from GenCC):

• myopathy, congenital, progressive, with scoliosis

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina
• congenital myopathy with myasthenic-like onset

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135254.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX7	NM_001135254.2	MANE Select	c.1155+16029G>A		intron	N/A	NP_001128726.1
	PAX7	NM_002584.3		c.1155+16029G>A		intron	N/A	NP_002575.1
	PAX7	NM_013945.3		c.1149+16029G>A		intron	N/A	NP_039236.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX7	ENST00000420770.7	TSL:1 MANE Select	c.1155+16029G>A		intron	N/A	ENSP00000403389.2
	PAX7	ENST00000375375.7	TSL:1	c.1155+16029G>A		intron	N/A	ENSP00000364524.3
	PAX7	ENST00000400661.3	TSL:1	c.1149+16029G>A		intron	N/A	ENSP00000383502.3

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136336 AN: 152152 Hom.: 61169 Cov.: 33

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.895

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.896 AC: 136448 AN: 152270 Hom.: 61223 Cov.: 33 AF XY: 0.898 AC XY: 66837 AN XY: 74444

African (AFR) AF: 0.942 AC: 39146 AN: 41570

American (AMR) AF: 0.862 AC: 13190 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2995 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4718 AN: 5152

South Asian (SAS) AF: 0.890 AC: 4293 AN: 4822

European-Finnish (FIN) AF: 0.878 AC: 9315 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59790 AN: 68018

Other (OTH) AF: 0.894 AC: 1889 AN: 2114

Alfa AF: 0.877 Hom.: 17974

Bravo AF: 0.896

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs609959; hg19: chr1-19045819;